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Merge pull request #993 from xjrc/packages/metis

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Update Package : METIS/ParMETIS
This commit is contained in:
Todd Gamblin 2016-05-26 17:37:33 -05:00
commit 96f65479e7
3 changed files with 131 additions and 108 deletions
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5
.flake8
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@ -8,6 +8,9 @@
# - E221: multiple spaces before operator
# - E241: multiple spaces after ‘,’
#
# Let people use terse Python features:
# - E731 : lambda expressions
#
# Spack allows wildcard imports:
# - F403: disable wildcard import
#
@ -16,5 +19,5 @@
# - F999: name name be undefined or undefined from star imports.
#
[flake8]
ignore = E221,E241,F403,F821,F999
ignore = E221,E241,E731,F403,F821,F999
max-line-length = 79

190
var/spack/repos/builtin/packages/metis/package.py
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@ -24,55 +24,61 @@
##############################################################################
from spack import *
import glob, sys, os
import glob
import sys
import os
class Metis(Package):
"""
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill
reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel
recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
"""
"""METIS is a set of serial programs for partitioning graphs, partitioning
finite element meshes, and producing fill reducing orderings for sparse
matrices. The algorithms implemented in METIS are based on the
multilevel recursive-bisection, multilevel k-way, and multi-constraint
partitioning schemes."""
homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview'
url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz"
homepage = "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview"
base_url = "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis"
version('5.1.0', '5465e67079419a69e0116de24fce58fe',
url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz')
version('4.0.3', '5efa35de80703c1b2c4d0de080fafbcf4e0d363a21149a1ad2f96e0144841a55',
url='http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD/metis-4.0.3.tar.gz')
version('5.1.0', '5465e67079419a69e0116de24fce58fe')
version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
variant('idx64', default=False, description='Use int64_t as default index type')
variant('double', default=False, description='Use double precision floating point types')
variant('real64', default=False, description='Use double precision floating point types')
depends_on('cmake @2.8:', when='@5:') # build-time dependency
depends_on('gdb', when='+gdb')
depends_on('cmake@2.8:', when='@5:') # build-time dependency
patch('install_gklib_defs_rename.patch', when='@5:')
def url_for_version(self, version):
verdir = 'OLD/' if version < Version('4.0.3') else ''
return '%s/%smetis-%s.tar.gz' % (Metis.base_url, verdir, version)
@when('@4:4.0.3')
@when('@:4')
def install(self, spec, prefix):
if '+gdb' in spec:
raise InstallError('gdb support not implemented in METIS 4!')
if '+idx64' in spec:
raise InstallError('idx64 option not implemented in METIS 4!')
if '+double' in spec:
raise InstallError('double option not implemented for METIS 4!')
# Process library spec and options
unsupp_vars = [v for v in ('+gdb', '+idx64', '+real64') if v in spec]
if unsupp_vars:
msg = 'Given variants %s are unsupported by METIS 4!' % unsupp_vars
raise InstallError(msg)
options = ['COPTIONS=-fPIC']
if '+debug' in spec:
options.append('OPTFLAGS=-g -O0')
make(*options)
# Compile and install library files
ccompile = Executable(self.compiler.cc)
mkdir(prefix.bin)
for x in ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk'):
install(x, prefix.bin)
binfiles = ('pmetis', 'kmetis', 'oemetis', 'onmetis', 'partnmesh',
'partdmesh', 'mesh2nodal', 'mesh2dual', 'graphchk')
for binfile in binfiles:
install(binfile, prefix.bin)
mkdir(prefix.lib)
install('libmetis.a', prefix.lib)
@ -82,106 +88,120 @@ def install(self, spec, prefix):
install(h, prefix.include)
mkdir(prefix.share)
for f in (join_path(*p)
for p in (('Programs', 'io.c'),
('Test','mtest.c'),
('Graphs','4elt.graph'),
('Graphs', 'metis.mesh'),
('Graphs', 'test.mgraph'))):
install(f, prefix.share)
sharefiles = (('Graphs', '4elt.graph'), ('Graphs', 'metis.mesh'),
('Graphs', 'test.mgraph'))
for sharefile in tuple(join_path(*sf) for sf in sharefiles):
install(sharefile, prefix.share)
if '+shared' in spec:
shared_flags = ['-fPIC', '-shared']
if sys.platform == 'darwin':
lib_dsuffix = 'dylib'
load_flag = '-Wl,-all_load'
no_load_flag = ''
shared_suffix = 'dylib'
shared_flags.extend(['-Wl,-all_load', 'libmetis.a'])
else:
lib_dsuffix = 'so'
load_flag = '-Wl,-whole-archive'
no_load_flag = '-Wl,-no-whole-archive'
shared_suffix = 'so'
shared_flags.extend(['-Wl,-whole-archive', 'libmetis.a',
'-Wl,-no-whole-archive'])
os.system(spack_cc + ' -fPIC -shared ' + load_flag +
' libmetis.a ' + no_load_flag + ' -o libmetis.' +
lib_dsuffix)
install('libmetis.' + lib_dsuffix, prefix.lib)
shared_out = '%s/libmetis.%s' % (prefix.lib, shared_suffix)
shared_flags.extend(['-o', shared_out])
ccompile(*shared_flags)
# Set up and run tests on installation
symlink(join_path(prefix.share, 'io.c'), 'io.c')
symlink(join_path(prefix.share, 'mtest.c'), 'mtest.c')
os.system(spack_cc + ' -I%s' % prefix.include + ' -c io.c')
os.system(spack_cc + ' -I%s' % prefix.include +
' -L%s' % prefix.lib + ' -lmetis mtest.c io.o -o mtest')
_4eltgraph = join_path(prefix.share, '4elt.graph')
test_mgraph = join_path(prefix.share, 'test.mgraph')
metis_mesh = join_path(prefix.share, 'metis.mesh')
kmetis = join_path(prefix.bin, 'kmetis')
os.system('./mtest ' + _4eltgraph)
os.system(kmetis + ' ' + _4eltgraph + ' 40')
os.system(join_path(prefix.bin, 'onmetis') + ' ' + _4eltgraph)
os.system(join_path(prefix.bin, 'pmetis') + ' ' + test_mgraph + ' 2')
os.system(kmetis + ' ' + test_mgraph + ' 2')
os.system(kmetis + ' ' + test_mgraph + ' 5')
os.system(join_path(prefix.bin, 'partnmesh') + metis_mesh + ' 10')
os.system(join_path(prefix.bin, 'partdmesh') + metis_mesh + ' 10')
os.system(join_path(prefix.bin, 'mesh2dual') + metis_mesh)
ccompile('-I%s' % prefix.include, '-L%s' % prefix.lib,
'-Wl,-rpath=%s' % (prefix.lib if '+shared' in spec else ''),
join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
'-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
test_bin = lambda testname: join_path(prefix.bin, testname)
test_graph = lambda graphname: join_path(prefix.share, graphname)
graph = test_graph('4elt.graph')
os.system('%s %s' % (test_bin('mtest'), graph))
os.system('%s %s 40' % (test_bin('kmetis'), graph))
os.system('%s %s' % (test_bin('onmetis'), graph))
graph = test_graph('test.mgraph')
os.system('%s %s 2' % (test_bin('pmetis'), graph))
os.system('%s %s 2' % (test_bin('kmetis'), graph))
os.system('%s %s 5' % (test_bin('kmetis'), graph))
graph = test_graph('metis.mesh')
os.system('%s %s 10' % (test_bin('partnmesh'), graph))
os.system('%s %s 10' % (test_bin('partdmesh'), graph))
os.system('%s %s' % (test_bin('mesh2dual'), graph))
# FIXME: The following code should replace the testing code in the
# block above since it causes installs to fail when one or more of the
# Metis tests fail, but it currently doesn't work because the 'mtest',
# 'onmetis', and 'partnmesh' tests return error codes that trigger
# false positives for failure.
"""
Executable(test_bin('mtest'))(test_graph('4elt.graph'))
Executable(test_bin('kmetis'))(test_graph('4elt.graph'), '40')
Executable(test_bin('onmetis'))(test_graph('4elt.graph'))
Executable(test_bin('pmetis'))(test_graph('test.mgraph'), '2')
Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '2')
Executable(test_bin('kmetis'))(test_graph('test.mgraph'), '5')
Executable(test_bin('partnmesh'))(test_graph('metis.mesh'), '10')
Executable(test_bin('partdmesh'))(test_graph('metis.mesh'), '10')
Executable(test_bin('mesh2dual'))(test_graph('metis.mesh'))
"""
@when('@5:')
def install(self, spec, prefix):
options = []
options.extend(std_cmake_args)
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory))
options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
if '+shared' in spec:
options.append('-DSHARED:BOOL=ON')
if '+debug' in spec:
options.extend(['-DDEBUG:BOOL=ON',
'-DCMAKE_BUILD_TYPE:STRING=Debug'])
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
metis_header = join_path(source_directory, 'include', 'metis.h')
if '+idx64' in spec:
filter_file('IDXTYPEWIDTH 32', 'IDXTYPEWIDTH 64', metis_header)
if '+double' in spec:
if '+real64' in spec:
filter_file('REALTYPEWIDTH 32', 'REALTYPEWIDTH 64', metis_header)
# Make clang 7.3 happy.
# Prevents "ld: section __DATA/__thread_bss extends beyond end of file"
# See upstream LLVM issue https://llvm.org/bugs/show_bug.cgi?id=27059
# Adopted from https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
# and https://github.com/Homebrew/homebrew-science/blob/master/metis.rb
if spec.satisfies('%clang@7.3.0'):
filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24', join_path(source_directory, 'GKlib', 'error.c'))
filter_file('#define MAX_JBUFS 128', '#define MAX_JBUFS 24',
join_path(source_directory, 'GKlib', 'error.c'))
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
# now run some tests:
for f in ["4elt", "copter2", "mdual"]:
graph = join_path(source_directory,'graphs','%s.graph' % f)
Executable(join_path(prefix.bin,'graphchk'))(graph)
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
Executable(join_path(prefix.bin,'ndmetis'))(graph)
make('install')
graph = join_path(source_directory,'graphs','test.mgraph')
Executable(join_path(prefix.bin,'gpmetis'))(graph,'2')
graph = join_path(source_directory,'graphs','metis.mesh')
Executable(join_path(prefix.bin,'mpmetis'))(graph,'2')
# now run some tests:
for f in ['4elt', 'copter2', 'mdual']:
graph = join_path(source_directory, 'graphs', '%s.graph' % f)
Executable(join_path(prefix.bin, 'graphchk'))(graph)
Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
Executable(join_path(prefix.bin, 'ndmetis'))(graph)
graph = join_path(source_directory, 'graphs', 'test.mgraph')
Executable(join_path(prefix.bin, 'gpmetis'))(graph, '2')
graph = join_path(source_directory, 'graphs', 'metis.mesh')
Executable(join_path(prefix.bin, 'mpmetis'))(graph, '2')
# install GKlib headers, which will be needed for ParMETIS
GKlib_dist = join_path(prefix.include,'GKlib')
GKlib_dist = join_path(prefix.include, 'GKlib')
mkdirp(GKlib_dist)
fs = glob.glob(join_path(source_directory,'GKlib',"*.h"))
for f in fs:
install(f, GKlib_dist)
hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
for hfile in hfiles:
install(hfile, GKlib_dist)

44
var/spack/repos/builtin/packages/parmetis/package.py
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@ -26,33 +26,36 @@
from spack import *
import sys
class Parmetis(Package):
"""
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured
graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
"""
"""ParMETIS is an MPI-based parallel library that implements a variety of
algorithms for partitioning unstructured graphs, meshes, and for
computing fill-reducing orderings of sparse matrices."""
homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview'
url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz'
base_url = 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis'
version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
variant('shared', default=True, description='Enables the build of shared libraries')
variant('debug', default=False, description='Builds the library in debug mode')
variant('gdb', default=False, description='Enables gdb support')
depends_on('cmake @2.8:') # build dependency
depends_on('cmake@2.8:') # build dependency
depends_on('mpi')
patch('enable_external_metis.patch')
depends_on('metis@5:')
patch('enable_external_metis.patch')
# bug fixes from PETSc developers
# https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
# https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/ # NOQA: ignore=E501
patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
# https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
# https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/ # NOQA: ignore=E501
patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
depends_on('gdb', when='+gdb')
def url_for_version(self, version):
verdir = 'OLD/' if version < Version('3.2.0') else ''
return '%s/%sparmetis-%s.tar.gz' % (Parmetis.base_url, verdir, version)
def install(self, spec, prefix):
options = []
@ -60,30 +63,27 @@ def install(self, spec, prefix):
build_directory = join_path(self.stage.path, 'spack-build')
source_directory = self.stage.source_path
metis_source = join_path(source_directory, 'metis')
# FIXME : Once a contract is defined, MPI compilers should be retrieved indirectly via spec['mpi'] in case
# FIXME : they use a non-standard name
options.extend(['-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=spec['metis'].prefix.include),
'-DMETIS_PATH:PATH={metis_source}'.format(metis_source=spec['metis'].prefix),
'-DCMAKE_C_COMPILER:STRING=mpicc',
'-DCMAKE_CXX_COMPILER:STRING=mpicxx'])
options.extend([
'-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
'-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
'-DCMAKE_C_COMPILER:STRING=%s' % spec['mpi'].mpicc,
'-DCMAKE_CXX_COMPILER:STRING=%s' % spec['mpi'].mpicxx
])
if '+shared' in spec:
options.append('-DSHARED:BOOL=ON')
if '+debug' in spec:
options.extend(['-DDEBUG:BOOL=ON',
'-DCMAKE_BUILD_TYPE:STRING=Debug'])
if '+gdb' in spec:
options.append('-DGDB:BOOL=ON')
with working_dir(build_directory, create=True):
cmake(source_directory, *options)
make()
make("install")
make('install')
# The shared library is not installed correctly on Darwin; correct this
# The shared library is not installed correctly on Darwin; fix this
if (sys.platform == 'darwin') and ('+shared' in spec):
fix_darwin_install_name(prefix.lib)